Photoelectrocatalytic oxidation provides a technically applicable way for solar-chemical synthesis, but its efficiency and selectivity are moderate. Herein, a microfluidic photoelectrochemical architecture with 3-D microflow channels is constructed by interfacial engineering of defective WO3/TiO2 heterostructures on porous carbon fibers. Kelvin probe force microscopy and photoluminescence imaging visually evidence the charge accumulation sites on the nanojunction. This efficient charge separation contributes to a 3-fold enhancement in the yield of glyceraldehyde and 1,3-dihydroxyacetone during glycerol upgrading, together with nearly doubled production of high value-added KA oil and S2O82− oxidant through cyclohexane and HSO4− oxidization, respectively. More importantly, the microfluidic platform with enhanced mass transfer exhibits a typical reaction selectivity of 85 %, which is much higher than the conventional planar protocol. Integrating this microfluidic photoanode with an oxygen reduction cathode leads to a self-sustained photocatalytic fuel cell with remarkably high open-circuit voltage (0.9 V) and short-circuit current (1.2 mA cm−2)